Question: Redirecting the Log.txt file from a STAR indexing run
0
gravatar for cristian
3.5 years ago by
cristian240
cristian240 wrote:

When I run this command to index a genome with STAR:

STAR --runMode genomeGenerate --genomeDir output/genome/ecoli/index --genomeFastaFiles output/genome/ecoli/sequence/ecoli.fa --sjdbGTFfile output/genome/ecoli/annotation/ecoli.gtf > output/genome/ecoli/index/message.txt

a Log.txt file is created in my working directory with details about the indexation of the genome. Does anybody know how to write the Log.txt in another directory? Thanks. Cristian

index output star redirection • 2.0k views
ADD COMMENTlink modified 3.5 years ago by genomax78k • written 3.5 years ago by cristian240
2
gravatar for genomax
3.5 years ago by
genomax78k
United States
genomax78k wrote:

From STAR manual

STAR produces multiple output files. All files have standard name, however, you can change the file prefixes using --outFileNamePrefix /path/to/output/dir/prefix. By default, this parameter is ./, i.e. all output files are written in the current directory.

This would write all output files to the directory you specify.

If you only need to redirect stderr/stdout (as indicated in your command) then take a look at this.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by genomax78k

Thank you, it worked.

ADD REPLYlink written 3.5 years ago by cristian240
1

Thank you, it worked.

so, flag this question as answered please (green flag on the left)

ADD REPLYlink written 3.3 years ago by Pierre Lindenbaum126k
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